WGCNA: numbers2colors – R documentation

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WGCNA

numbers2colors

Color representation for a numeric variable

Description

The function creates a color represenation for the given numeric input.

Usage

numbers2colors(
   x, 
   signed = NULL, 
   centered = signed, 
   lim = NULL, 
   commonLim = FALSE,
   colors = if (signed) blueWhiteRed(100) else blueWhiteRed(100)[51:100],
   naColor = "grey")

Arguments

`x`	a vector or matrix of numbers. Missing values are allowed and will be assigned the color given in `naColor`. If a matrix, each column of the matrix is processed separately and the return value will be a matrix of colors.
`signed`	logical: should `x` be considered signed? If `TRUE`, the default setting is to use to use a palette that starts with green for the most negative values, continues with white for values around zero and turns red for positive values. If `FALSE`, the default palette ranges from white for minimum values to red for maximum values. If not given, the behaviour is controlled by values in `x`: if there are both positive and negative values, `signed` will be considered `TRUE`, otherwise `FALSE`.
`centered`	logical. If `TRUE` and `signed==TRUE`, numeric value zero will correspond to the middle of the color palette. If `FALSE` or `signed==FALSE`, the middle of the color palette will correspond to the average of the minimum and maximum value. If neither `signed` nor `centered` are given, `centered` will follow `signed` (see above).
`lim`	optional specification of limits, that is numeric values that should correspond to the first and last entry of `colors`.
`commonLim`	logical: should limits be calculated separately for each column of x, or should the limits be the same for all columns? Only applies if `lim` is `NULL`.
`colors`	color palette to represent the given numbers.
`naColor`	color to represent missing values in `x`.

Details

Each column of x is processed individually, meaning that the color palette is adjusted individually for each column of x.

Value

A vector or matrix (of the same dimensions as x) of colors.

Author(s)

Peter Langfelder